data_YMB
# 
_chem_comp.id                                    YMB 
_chem_comp.name                                  "7-[(1~{S})-1-[5-[(3-azanylazetidin-1-yl)methyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H29 F N4 O6 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-19 
_chem_comp.pdbx_modified_date                    2024-07-05 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        544.595 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YMB 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        8PGJ 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
YMB C11  C1  C 0 1 Y N N N N N -21.300 -11.944 8.523  2.802  -0.745 0.213  C11  YMB 1  
YMB C14  C2  C 0 1 Y N N N N N -20.096 -12.222 6.013  5.458  -0.276 -0.422 C14  YMB 2  
YMB C10  C3  C 0 1 Y N N N N N -21.901 -11.791 9.867  1.384  -0.995 0.553  C10  YMB 3  
YMB C12  C4  C 0 1 Y N N N N N -20.423 -10.980 8.034  3.804  -1.012 1.146  C12  YMB 4  
YMB C13  C5  C 0 1 Y N N N N N -19.855 -11.129 6.805  5.125  -0.777 0.824  C13  YMB 5  
YMB C17  C6  C 0 1 N N N N N N -20.738 -9.885  3.756  9.087  1.758  -0.805 C17  YMB 6  
YMB C15  C7  C 0 1 N N N N N N -19.461 -12.388 4.653  6.902  -0.022 -0.767 C15  YMB 7  
YMB C01  C8  C 0 1 N N N N N N -22.944 -12.499 15.752 -3.991 -3.794 0.539  C01  YMB 8  
YMB C02  C9  C 0 1 N N S N N N -23.517 -12.030 14.406 -3.149 -2.558 0.861  C02  YMB 9  
YMB C03  C10 C 0 1 Y N N N N N -22.851 -12.820 13.224 -1.810 -2.671 0.179  C03  YMB 10 
YMB C04  C11 C 0 1 Y N N N N N -22.571 -12.165 12.001 -0.754 -1.853 0.574  C04  YMB 11 
YMB C06  C12 C 0 1 Y N N N N N -22.410 -10.621 10.417 0.638  -0.349 1.523  C06  YMB 12 
YMB C07  C13 C 0 1 N N N N N N -22.710 -9.309  9.820  1.126  0.718  2.401  C07  YMB 13 
YMB C20  C14 C 0 1 Y N N N N N -20.941 -13.179 6.544  4.469  -0.014 -1.356 C20  YMB 14 
YMB C22  C15 C 0 1 Y N N N N N -21.539 -13.064 7.782  3.142  -0.246 -1.045 C22  YMB 15 
YMB C23  C16 C 0 1 Y N N N N N -21.977 -12.776 10.888 0.489  -1.974 -0.075 C23  YMB 16 
YMB C24  C17 C 0 1 Y N N N N N -21.631 -14.160 10.977 0.651  -2.907 -1.102 C24  YMB 17 
YMB C25  C18 C 0 1 Y N N N N N -21.915 -14.814 12.179 -0.398 -3.699 -1.472 C25  YMB 18 
YMB C26  C19 C 0 1 Y N N N N N -22.529 -14.178 13.265 -1.627 -3.583 -0.836 C26  YMB 19 
YMB C28  C20 C 0 1 N N N N N N -25.753 -13.169 15.067 -4.306 -0.246 1.226  C28  YMB 20 
YMB C29  C21 C 0 1 N N N N N N -27.077 -13.005 14.567 -4.953 0.732  0.226  C29  YMB 21 
YMB C30  C22 C 0 1 N N N N N N -28.239 -13.913 14.993 -6.438 0.919  0.543  C30  YMB 22 
YMB C32  C23 C 0 1 N N N N N N -29.280 -12.929 16.807 -6.948 3.247  0.069  C32  YMB 23 
YMB C33  C24 C 0 1 N N N N N N -30.730 -13.329 16.903 -8.389 3.406  -0.447 C33  YMB 24 
YMB C35  C25 C 0 1 N N N N N N -30.574 -13.951 15.553 -8.505 1.878  -0.301 C35  YMB 25 
YMB C37  C26 C 0 1 N N N N N N -25.841 -11.483 13.472 -4.150 -1.093 -0.893 C37  YMB 26 
YMB F21  F1  F 0 1 N N N N N N -21.214 -14.268 5.782  4.801  0.475  -2.571 F21  YMB 27 
YMB N05  N1  N 0 1 Y N N N N N -22.774 -10.864 11.665 -0.640 -0.870 1.529  N05  YMB 28 
YMB N27  N2  N 0 1 N N N N N N -24.989 -12.186 14.405 -3.840 -1.358 0.383  N27  YMB 29 
YMB N31  N3  N 0 1 N N N N N N -29.354 -13.107 15.316 -7.031 1.854  -0.422 N31  YMB 30 
YMB N34  N4  N 0 1 N N N N N N -31.588 -12.134 17.003 -8.472 3.875  -1.837 N34  YMB 31 
YMB O08  O1  O 0 1 N N N N N N -23.195 -9.296  8.624  2.276  1.103  2.309  O08  YMB 32 
YMB O09  O2  O 0 1 N N N N N N -22.598 -8.248  10.490 0.299  1.273  3.312  O09  YMB 33 
YMB O18  O3  O 0 1 N N N N N N -21.752 -12.257 3.358  7.268  1.800  1.104  O18  YMB 34 
YMB O19  O4  O 0 1 N N N N N N -19.828 -11.630 2.126  6.600  2.573  -1.125 O19  YMB 35 
YMB O36  O5  O 0 1 N N N N N N -27.146 -11.987 13.637 -4.785 0.078  -1.065 O36  YMB 36 
YMB O38  O6  O 0 1 N N N N N N -25.542 -10.578 12.801 -3.882 -1.842 -1.812 O38  YMB 37 
YMB S16  S1  S 0 1 N N N N N N -20.470 -11.605 3.374  7.343  1.677  -0.310 S16  YMB 38 
YMB H121 H1  H 0 0 N N N N N N -20.192 -10.110 8.631  3.546  -1.402 2.120  H121 YMB 39 
YMB H131 H2  H 0 0 N N N N N N -19.191 -10.359 6.441  5.900  -0.984 1.546  H131 YMB 40 
YMB H171 H3  H 0 0 N N N N N N -21.242 -9.799  4.730  9.655  1.006  -0.257 H171 YMB 41 
YMB H172 H4  H 0 0 N N N N N N -19.770 -9.363  3.797  9.170  1.568  -1.875 H172 YMB 42 
YMB H173 H5  H 0 0 N N N N N N -21.367 -9.430  2.977  9.483  2.748  -0.580 H173 YMB 43 
YMB H152 H6  H 0 0 N N N N N N -19.363 -13.461 4.429  7.535  -0.721 -0.220 H152 YMB 44 
YMB H151 H7  H 0 0 N N N N N N -18.464 -11.923 4.661  7.050  -0.160 -1.838 H151 YMB 45 
YMB H011 H8  H 0 0 N N N N N N -23.420 -11.937 16.569 -4.137 -3.863 -0.539 H011 YMB 46 
YMB H013 H9  H 0 0 N N N N N N -23.143 -13.573 15.881 -3.477 -4.687 0.894  H013 YMB 47 
YMB H012 H10 H 0 0 N N N N N N -21.858 -12.323 15.770 -4.960 -3.712 1.032  H012 YMB 48 
YMB H021 H11 H 0 0 N N N N N N -23.271 -10.965 14.280 -3.003 -2.488 1.939  H021 YMB 49 
YMB H221 H12 H 0 0 N N N N N N -22.184 -13.845 8.157  2.371  -0.041 -1.773 H221 YMB 50 
YMB H241 H13 H 0 0 N N N N N N -21.169 -14.679 10.150 1.604  -3.002 -1.602 H241 YMB 51 
YMB H251 H14 H 0 0 N N N N N N -21.649 -15.856 12.275 -0.272 -4.420 -2.266 H251 YMB 52 
YMB H261 H15 H 0 0 N N N N N N -22.758 -14.749 14.152 -2.448 -4.216 -1.140 H261 YMB 53 
YMB H281 H16 H 0 0 N N N N N N -25.374 -14.175 14.835 -3.467 0.227  1.735  H281 YMB 54 
YMB H1   H17 H 0 1 N N N N N N -25.728 -13.010 16.155 -5.043 -0.597 1.949  H1   YMB 55 
YMB H2   H18 H 0 1 N N N N N N -27.312 -12.300 15.378 -4.436 1.691  0.242  H2   YMB 56 
YMB H301 H19 H 0 0 N N N N N N -28.500 -14.591 14.167 -6.948 -0.043 0.478  H301 YMB 57 
YMB H302 H20 H 0 0 N N N N N N -27.943 -14.504 15.872 -6.547 1.320  1.551  H302 YMB 58 
YMB H321 H21 H 0 0 N N N N N N -28.586 -13.618 17.311 -6.220 3.858  -0.466 H321 YMB 59 
YMB H322 H22 H 0 0 N N N N N N -29.073 -11.898 17.130 -6.857 3.328  1.152  H322 YMB 60 
YMB H331 H23 H 0 0 N N N N N N -30.917 -14.067 17.697 -9.038 3.964  0.229  H331 YMB 61 
YMB H351 H24 H 0 0 N N N N N N -31.406 -13.745 14.863 -8.871 1.557  0.675  H351 YMB 62 
YMB H352 H25 H 0 0 N N N N N N -30.376 -15.033 15.576 -9.024 1.396  -1.129 H352 YMB 63 
YMB H051 H26 H 0 0 N N N N N N -23.152 -10.176 12.284 -1.354 -0.584 2.120  H051 YMB 64 
YMB H341 H28 H 0 0 N N N N N N -31.609 -11.817 17.951 -9.433 3.964  -2.132 H341 YMB 65 
YMB H342 H29 H 0 0 N N N N N N -31.221 -11.411 16.418 -7.975 4.745  -1.955 H342 YMB 66 
YMB H5   H31 H 0 1 N N N N N N -22.915 -7.514  9.977  0.710  1.968  3.844  H5   YMB 67 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
YMB O19 S16  DOUB N N 1  
YMB O18 S16  DOUB N N 2  
YMB S16 C17  SING N N 3  
YMB S16 C15  SING N N 4  
YMB C15 C14  SING N N 5  
YMB F21 C20  SING N N 6  
YMB C14 C20  DOUB Y N 7  
YMB C14 C13  SING Y N 8  
YMB C20 C22  SING Y N 9  
YMB C13 C12  DOUB Y N 10 
YMB C22 C11  DOUB Y N 11 
YMB C12 C11  SING Y N 12 
YMB C11 C10  SING N N 13 
YMB O08 C07  DOUB N N 14 
YMB C07 C06  SING N N 15 
YMB C07 O09  SING N N 16 
YMB C10 C06  DOUB Y N 17 
YMB C10 C23  SING Y N 18 
YMB C06 N05  SING Y N 19 
YMB C23 C24  DOUB Y N 20 
YMB C23 C04  SING Y N 21 
YMB C24 C25  SING Y N 22 
YMB N05 C04  SING Y N 23 
YMB C04 C03  DOUB Y N 24 
YMB C25 C26  DOUB Y N 25 
YMB O38 C37  DOUB N N 26 
YMB C03 C26  SING Y N 27 
YMB C03 C02  SING N N 28 
YMB C37 O36  SING N N 29 
YMB C37 N27  SING N N 30 
YMB O36 C29  SING N N 31 
YMB N27 C02  SING N N 32 
YMB N27 C28  SING N N 33 
YMB C02 C01  SING N N 34 
YMB C29 C30  SING N N 35 
YMB C29 C28  SING N N 36 
YMB C30 N31  SING N N 37 
YMB N31 C35  SING N N 38 
YMB N31 C32  SING N N 39 
YMB C35 C33  SING N N 40 
YMB C32 C33  SING N N 41 
YMB C33 N34  SING N N 42 
YMB C12 H121 SING N N 43 
YMB C13 H131 SING N N 44 
YMB C17 H171 SING N N 45 
YMB C17 H172 SING N N 46 
YMB C17 H173 SING N N 47 
YMB C15 H152 SING N N 48 
YMB C15 H151 SING N N 49 
YMB C01 H011 SING N N 50 
YMB C01 H013 SING N N 51 
YMB C01 H012 SING N N 52 
YMB C02 H021 SING N N 53 
YMB C22 H221 SING N N 54 
YMB C24 H241 SING N N 55 
YMB C25 H251 SING N N 56 
YMB C26 H261 SING N N 57 
YMB C28 H281 SING N N 58 
YMB C28 H1   SING N N 59 
YMB C29 H2   SING N N 60 
YMB C30 H301 SING N N 61 
YMB C30 H302 SING N N 62 
YMB C32 H321 SING N N 63 
YMB C32 H322 SING N N 64 
YMB C33 H331 SING N N 65 
YMB C35 H351 SING N N 66 
YMB C35 H352 SING N N 67 
YMB N05 H051 SING N N 68 
YMB N34 H341 SING N N 69 
YMB N34 H342 SING N N 70 
YMB O09 H5   SING N N 71 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
YMB InChI            InChI                1.06  "InChI=1S/C26H29FN4O6S/c1-14(31-12-18(37-26(31)34)11-30-9-17(28)10-30)19-4-3-5-20-22(24(25(32)33)29-23(19)20)15-6-7-16(21(27)8-15)13-38(2,35)36/h3-8,14,17-18,29H,9-13,28H2,1-2H3,(H,32,33)/t14-,18-/m0/s1" 
YMB InChIKey         InChI                1.06  AELVYVNWNWJKTP-KSSFIOAISA-N                                                                                                                                                                                 
YMB SMILES_CANONICAL CACTVS               3.385 "C[C@H](N1C[C@H](CN2CC(N)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4c5ccc(C[S](C)(=O)=O)c(F)c5"                                                                                                                       
YMB SMILES           CACTVS               3.385 "C[CH](N1C[CH](CN2CC(N)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4c5ccc(C[S](C)(=O)=O)c(F)c5"                                                                                                                         
YMB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](c1cccc2c1[nH]c(c2c3ccc(c(c3)F)CS(=O)(=O)C)C(=O)O)N4CC(OC4=O)CN5CC(C5)N"                                                                                                                            
YMB SMILES           "OpenEye OEToolkits" 2.0.7 "CC(c1cccc2c1[nH]c(c2c3ccc(c(c3)F)CS(=O)(=O)C)C(=O)O)N4CC(OC4=O)CN5CC(C5)N"                                                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           YMB 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "7-[(1~{S})-1-[5-[(3-azanylazetidin-1-yl)methyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-carboxylic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YMB "Create component" 2023-06-20 PDBE 
YMB "Initial release"  2024-07-10 RCSB 
# 
